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Package 343/565HostnameOS / ArchBUILDCHECKBUILD BIN
MEDIPS 1.7.0
Lukas Chavez
Snapshot Date: 2012-06-20 15:22:40 -0700 (Wed, 20 Jun 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MEDIPS
Last Changed Rev: 64680 / Revision: 66885
Last Changed Date: 2012-03-30 15:15:56 -0700 (Fri, 30 Mar 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: MEDIPS
Version: 1.7.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MEDIPS_1.7.0.tar.gz
StartedAt: 2012-06-21 01:36:39 -0700 (Thu, 21 Jun 2012)
EndedAt: 2012-06-21 01:49:56 -0700 (Thu, 21 Jun 2012)
EllapsedTime: 797.4 seconds
RetCode: 0
Status:  OK 
CheckDir: MEDIPS.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/MEDIPS.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'MEDIPS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MEDIPS' version '1.7.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'MEDIPS' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 47.7Mb
  sub-directories of 1Mb or more:
    extdata  47.0Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/MEDIPS.Rcheck/00check.log'
for details.

MEDIPS.Rcheck/00install.out:

* installing *source* package 'MEDIPS' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c annotate.c -o annotate.o
annotate.c: In function 'annotate':
annotate.c:21: warning: suggest parentheses around comparison in operand of &
annotate.c:32: warning: suggest parentheses around comparison in operand of &
annotate.c:43: warning: suggest parentheses around comparison in operand of &
annotate.c:8: warning: unused variable 'rj'
annotate.c:8: warning: unused variable 'aj'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c calibration.c -o calibration.o
calibration.c: In function 'calibration':
calibration.c:10: warning: suggest parentheses around comparison in operand of &
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c coupling.c -o coupling.o
coupling.c: In function 'coupling':
coupling.c:26: warning: statement with no effect
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c profile.c -o profile.o
profile.c: In function 'profile':
profile.c:42: warning: unused variable 'wie'
profile.c:221: warning: suggest parentheses around comparison in operand of &
profile.c:221: warning: suggest parentheses around comparison in operand of &
profile.c:221: warning: suggest parentheses around comparison in operand of &
profile.c:221: warning: suggest parentheses around comparison in operand of &
profile.c:227: warning: suggest parentheses around comparison in operand of &
profile.c:227: warning: suggest parentheses around comparison in operand of &
profile.c:227: warning: suggest parentheses around comparison in operand of &
profile.c:227: warning: suggest parentheses around comparison in operand of &
profile.c:263: warning: suggest parentheses around comparison in operand of &
profile.c:263: warning: suggest parentheses around comparison in operand of &
profile.c:263: warning: suggest parentheses around comparison in operand of &
profile.c:263: warning: suggest parentheses around comparison in operand of &
profile.c:269: warning: suggest parentheses around comparison in operand of &
profile.c:269: warning: suggest parentheses around comparison in operand of &
profile.c:269: warning: suggest parentheses around comparison in operand of &
profile.c:269: warning: suggest parentheses around comparison in operand of &
profile.c:34: warning: unused variable 'items'
profile.c:11: warning: unused variable 'pvalue'
profile.c:11: warning: unused variable 'Val'
profile.c:25: warning: 'ptrgenome_norm2' may be used uninitialized in this function
profile.c:25: warning: 'ptrgenome_raw2' may be used uninitialized in this function
profile.c:13: warning: 'ptr_input' may be used uninitialized in this function
profile.c:11: warning: 'nY' may be used uninitialized in this function
profile.c:11: warning: 'Y' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c roiprofile.c -o roiprofile.o
roiprofile.c: In function 'calculate':
roiprofile.c:181: warning: suggest parentheses around comparison in operand of &
roiprofile.c:181: warning: suggest parentheses around comparison in operand of &
roiprofile.c:181: warning: suggest parentheses around comparison in operand of &
roiprofile.c:181: warning: suggest parentheses around comparison in operand of &
roiprofile.c:186: warning: suggest parentheses around comparison in operand of &
roiprofile.c:186: warning: suggest parentheses around comparison in operand of &
roiprofile.c:186: warning: suggest parentheses around comparison in operand of &
roiprofile.c:186: warning: suggest parentheses around comparison in operand of &
roiprofile.c:221: warning: suggest parentheses around comparison in operand of &
roiprofile.c:221: warning: suggest parentheses around comparison in operand of &
roiprofile.c:221: warning: suggest parentheses around comparison in operand of &
roiprofile.c:221: warning: suggest parentheses around comparison in operand of &
roiprofile.c:226: warning: suggest parentheses around comparison in operand of &
roiprofile.c:226: warning: suggest parentheses around comparison in operand of &
roiprofile.c:226: warning: suggest parentheses around comparison in operand of &
roiprofile.c:226: warning: suggest parentheses around comparison in operand of &
roiprofile.c:12: warning: unused variable 'Val'
roiprofile.c: In function 'roiprofile':
roiprofile.c:280: warning: suggest parentheses around comparison in operand of &
roiprofile.c:282: warning: suggest parentheses around comparison in operand of &
roiprofile.c:294: warning: suggest parentheses around comparison in operand of &
roiprofile.c:296: warning: suggest parentheses around comparison in operand of &
roiprofile.c:248: warning: unused variable 'nProtected'
roiprofile.c: In function 'calculate':
roiprofile.c:29: warning: 'ptrinput' may be used uninitialized in this function
roiprofile.c:29: warning: 'IN' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o MEDIPS.so annotate.o calibration.o coupling.o profile.o roiprofile.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/MEDIPS.Rcheck/MEDIPS/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'MEDIPS.Rnw' 
** testing if installed package can be loaded

* DONE (MEDIPS)

MEDIPS.Rcheck/MEDIPS-Ex.timings:

nameusersystemelapsed
MEDIPS.CpGenrich186.349 20.070216.369
MEDIPS.annotate0.0540.0060.058
MEDIPS.calibrationCurve7.4401.9089.472
MEDIPS.couplingVector6.2421.5277.859
MEDIPS.coverageAnalysis14.473 4.69919.970
MEDIPS.exportWIG6.8401.3818.438
MEDIPS.genomeVector4.4451.0735.567
MEDIPS.getPositions3.5730.5384.173
MEDIPS.mergeFrames0.0080.0010.009
MEDIPS.methylProfiling10.566 2.21812.988
MEDIPS.normalize 8.311 2.13010.584
MEDIPS.plotCalibrationPlot11.624 2.09214.003
MEDIPS.plotCoverage16.236 4.53120.977
MEDIPS.plotSaturation60.380 2.16463.102
MEDIPS.readAlignedSequences2.7700.3593.165
MEDIPS.saturationAnalysis64.072 2.31067.598
MEDIPS.selectSignificants140.787 8.943152.206
MEDIPSset-class0.0020.0010.002